I am just curious why the output of the below bedops overlap command results some single gene per line and on others 2 or 3 or 4. Thank you :).
bedmap --echo --skip-unmapped --delim '\t' --echo-map-id-uniq unix_sort_4column_xgen_targets.bed sort_gene_exon.genecode.bed > answer.bed
chr1 979192 979413 + AGRN:exon.10
chr1 979478 979647 + AGRN:exon.11
chr1 979703 979829 + AGRN:exon.12
chr1 980530 980667 + AGRN:exon.13
chr1 980728 980913 + AGRN:exon.1;AGRN:exon.14
chr1 981102 981266 + AGRN:exon.15;AGRN:exon.2
chr1 981333 981478 + AGRN:exon.16;AGRN:exon.3
chr1 981529 981655 + AGRN:exon.17;AGRN:exon.4
1 answer
For some elements of the file unix_sort_4column_xgen_targets.bed, only one exon from the file sort_gene_exon.genecode.bed overlaps that element, and so one exon ID is reported.
For other elements of the file unix_sort_4column_xgen_targets.bed, two exons from the file sort_gene_exon.genecode.bed overlap that element, and so two exon IDs are reported.
Because you use the --skip-unmapped option, elements from unix_sort_4column_xgen_targets.bed that have zero overlaps with elements from sort_gene_exon.genecode.bed are not reported in the output file. You are skipping unmapped reference elements.
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written
by
Alex Reynolds
If the regions of exons 1 and 14 overlap that reference element, then yes. If you're not sure about your input data, do spot checks of specific elements. Also make sure that you are using BEDOPS sort-bed to sort your BED files, because 1) Unix sort is slower and 2) most uses of sort I see on this site do not sort on the third column, while sort-bed does.
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written
by
Alex Reynolds
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interval file for picard
written by bioguy24